In Uruguay, colonies of honey bees moving to Eucalyptus grandis plantation in autumn habitually become infected with the microsporidian Nosema ceranae, a parasite that attacks the digestive system of bees. Beekeepers attributed to N. ceranae depopulation of the colonies that often occurs at the end of the blooming period, and many use the antibiotic fumagillin to reduce the level of infection. The aim of this study was to compare the effectiveness of four different fumagillin treatments and determine how this antibiotic affects the strength of the colonies during the winter season. The colonies treated with fumagillin in July showed less spore load at the end of applications, being the most effective the following treatments: the four applications sprayed over bees of 30 mg of fumagillin in 100 ml of sugar syrup 1:1, and four applications of 90 mg of fumagillin in 250 ml of sugar syrup 1:1 using a feeder. However, 2 month after the treatment applications, the colonies treated with fumagillin were the same size as the untreated colonies. In September, the colonies treated and not treated with fumagillin did not differ in colony strength (adult bee population and brood area) or spores abundance. Our study demonstrates that fumagillin treatment temporarily decreased the spore load of N. ceranae, but this was not reflected in either the size of the colonies or the probability of surviving the winter regardless of the dose or the administration strategy applied. Given the results obtained, we suggest to not perform the pharmacological treatment under the conditions described in the experiment.